Merge branch 'develop' into tdrr-clean-refactor

Author: yardasol

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Tests and Coverage
 
 on:
   # allows us to run workflows manually
@@ -21,7 +21,25 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  filter-changes:
+    runs-on: ubuntu-latest
+    outputs:
+      source_changed: ${{ steps.filter.outputs.source_changed }}
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+      - name: Examine changed files
+        id: filter
+        uses: dorny/paths-filter@668c092af3649c4b664c54e4b704aa46782f6f7c # latest master commit, not released yet
+        with:
+          filters: |
+            source_changed:
+              - '!docs/**'
+              - '!**/*.md'
+          predicate-quantifier: 'every'
   main:
+    needs: filter-changes
+    if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
     runs-on: ubuntu-22.04
     strategy:
       matrix:
@@ -205,12 +223,33 @@ jobs:
           flag-name: C++ and Python
           path-to-lcov: coverage.lcov
 
-  finish:
-    needs: main
+  coverage:
+    needs: [filter-changes, main]
+    if: ${{ always() }}
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished
+        if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
         uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           parallel-finished: true
+
+  ci-pass:
+    needs: [filter-changes, main, coverage]
+    name: Check CI status
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check CI status
+        run: |
+          if [[ "${{ needs.filter-changes.outputs.source_changed }}" == "false" ]]; then
+            echo "Documentation-only change - CI skipped successfully"
+            exit 0
+          fi
+          if [[ "${{ needs.main.result }}" == "success" && "${{ needs.coverage.result }}" == "success" ]]; then
+            echo "CI passed"
+            exit 0
+          fi
+          echo "CI failed"
+          exit 1

AGENTS.md

@@ -31,6 +31,24 @@ C++17/Python codebase where:
 - **Depletion**: `openmc.deplete` implements burnup via operator-splitting with various integrators (Predictor, CECM, etc.)
 - **Nuclear Data**: `openmc.data` provides programmatic access to nuclear data files (ENDF, ACE, HDF5)
 
+## Git Branching Workflow
+
+OpenMC uses a git flow branching model with two primary branches:
+
+- **`develop` branch**: The main development branch where all ongoing development takes place. This is the **primary branch against which pull requests are submitted and merged**. This branch is not guaranteed to be stable and may contain work-in-progress features.
+- **`master` branch**: The stable release branch containing the latest stable release of OpenMC. This branch only receives merges from `develop` when the development team decides a release should occur.
+
+### Instructions for Code Review
+
+When analyzing code changes on a feature or bugfix branch (e.g., when a user asks "what do you think of these changes?"), **compare the branch changes against `develop`, not `master`**. Pull requests are submitted to merge into `develop`, so differences relative to `develop` represent the actual proposed changes. Comparing against `master` will include unrelated changes from other features that have already been merged to `develop`.
+
+### Workflow for contributors
+
+1. Create a feature/bugfix branch off `develop`
+2. Make changes and commit to the feature branch
+3. Open a pull request to merge the feature branch into `develop`
+4. A committer reviews and merges the PR into `develop`
+
 ## Critical Build & Test Workflows
 
 ### Build Dependencies

docs/source/usersguide/random_ray.rst

@@ -513,6 +513,7 @@ Supported scores:
     - total
     - fission
     - nu-fission
+    - kappa-fission
     - events
 
 Supported Estimators:

include/openmc/cell.h

@@ -123,11 +123,11 @@ class Region {
   //! BoundingBox if the particle is in a complex cell.
   BoundingBox bounding_box_complex(vector<int32_t> postfix) const;
 
-  //! Enfource precedence: Parenthases, Complement, Intersection, Union
-  void add_precedence();
+  //! Enforce precedence between intersections and unions
+  void enforce_precedence();
 
   //! Add parenthesis to enforce precedence
-  int64_t add_parentheses(int64_t start);
+  void add_parentheses(int64_t start);
 
   //! Remove complement operators from the expression
   void remove_complement_ops();

include/openmc/mesh.h

@@ -4,6 +4,7 @@
 #ifndef OPENMC_MESH_H
 #define OPENMC_MESH_H
 
+#include <set>
 #include <unordered_map>
 
 #include "hdf5.h"
@@ -969,7 +970,7 @@ class LibMesh : public UnstructuredMesh {
 
   Position sample_element(int32_t bin, uint64_t* seed) const override;
 
-  int get_bin(Position r) const override;
+  virtual int get_bin(Position r) const override;
 
   int n_bins() const override;
 
@@ -1007,16 +1008,21 @@ class LibMesh : public UnstructuredMesh {
 
 protected:
   // Methods
-
   //! Translate a bin value to an element reference
   virtual const libMesh::Elem& get_element_from_bin(int bin) const;
 
   //! Translate an element pointer to a bin index
   virtual int get_bin_from_element(const libMesh::Elem* elem) const;
 
+  // Data members
   libMesh::MeshBase* m_; //!< pointer to libMesh MeshBase instance, always set
                          //!< during intialization
+  vector<unique_ptr<libMesh::PointLocatorBase>>
+    pl_;                      //!< per-thread point locators
+  libMesh::BoundingBox bbox_; //!< bounding box of the mesh
+
 private:
+  // Methods
   void initialize() override;
   void set_mesh_pointer_from_filename(const std::string& filename);
   void build_eqn_sys();
@@ -1025,8 +1031,6 @@ class LibMesh : public UnstructuredMesh {
   unique_ptr<libMesh::MeshBase> unique_m_ =
     nullptr; //!< pointer to the libMesh MeshBase instance, only used if mesh is
              //!< created inside OpenMC
-  vector<unique_ptr<libMesh::PointLocatorBase>>
-    pl_; //!< per-thread point locators
   unique_ptr<libMesh::EquationSystems>
     equation_systems_; //!< pointer to the libMesh EquationSystems
                        //!< instance
@@ -1035,16 +1039,16 @@ class LibMesh : public UnstructuredMesh {
   std::unordered_map<std::string, unsigned int>
     variable_map_; //!< mapping of variable names (tally scores) to libMesh
                    //!< variable numbers
-  libMesh::BoundingBox bbox_; //!< bounding box of the mesh
   libMesh::dof_id_type
     first_element_id_; //!< id of the first element in the mesh
 };
 
 class AdaptiveLibMesh : public LibMesh {
 public:
   // Constructor
-  AdaptiveLibMesh(
-    libMesh::MeshBase& input_mesh, double length_multiplier = 1.0);
+  AdaptiveLibMesh(libMesh::MeshBase& input_mesh, double length_multiplier = 1.0,
+    const std::set<libMesh::subdomain_id_type>& block_ids =
+      std::set<libMesh::subdomain_id_type>());
 
   // Overridden methods
   int n_bins() const override;
@@ -1056,6 +1060,8 @@ class AdaptiveLibMesh : public LibMesh {
 
   void write(const std::string& filename) const override;
 
+  int get_bin(Position r) const override;
+
 protected:
   // Overridden methods
   int get_bin_from_element(const libMesh::Elem* elem) const override;
@@ -1064,6 +1070,9 @@ class AdaptiveLibMesh : public LibMesh {
 
 private:
   // Data members
+  const std::set<libMesh::subdomain_id_type>
+    block_ids_;               //!< subdomains of the mesh to tally on
+  const bool block_restrict_; //!< whether a subset of the mesh is being used
   const libMesh::dof_id_type num_active_; //!< cached number of active elements
 
   std::vector<libMesh::dof_id_type>

include/openmc/random_ray/flat_source_domain.h

@@ -138,6 +138,7 @@ class FlatSourceDomain {
   vector<double> nu_sigma_f_;
   vector<double> sigma_f_;
   vector<double> chi_;
+  vector<double> kappa_fission_;
 
   // 3D arrays stored in 1D representing values for all materials x energy
   // groups x energy groups

include/openmc/random_ray/random_ray_simulation.h

@@ -21,10 +21,8 @@ class RandomRaySimulation {
   // Methods
   void apply_fixed_sources_and_mesh_domains();
   void prepare_fixed_sources_adjoint();
-  void run_single_simulation();
-  void random_ray_adjoint();
-  void kinetic_initial_condition();
   void kinetic_single_time_step(int i);
+  void prepare_adjoint_simulation();
   void simulate();
   void output_simulation_results() const;
   void instability_check(
@@ -35,9 +33,15 @@ class RandomRaySimulation {
   // Accessors
   FlatSourceDomain* domain() const { return domain_.get(); }
 
+  //----------------------------------------------------------------------------
+  // Public data members
+
+  // Flag for adjoint simulation;
+  bool adjoint_needed_;
+
 private:
   //----------------------------------------------------------------------------
-  // Data Members
+  // Private data members
 
   // Contains all flat source region data
   unique_ptr<FlatSourceDomain> domain_;
@@ -58,9 +62,6 @@ class RandomRaySimulation {
   // Toggle for first simulation
   bool is_first_simulation_;
 
-  // Flag for adjoint simulation;
-  bool adjoint_needed_;
-
   //----------------------------------------------------------------------------
   // Data Members for kinetic simulations
 
@@ -77,6 +78,7 @@ class RandomRaySimulation {
 void openmc_run_random_ray();
 void validate_random_ray_inputs();
 void openmc_reset_random_ray();
+void print_adjoint_header();
 
 //! Write data related to randaom ray to statepoint
 //! \param[in] group HDF5 group

openmc/data/photon.py

@@ -203,7 +203,9 @@ def transitions(self, transitions):
         for subshell, df in transitions.items():
             cv.check_value('subshell', subshell, _SUBSHELLS)
             cv.check_type('transitions', df, pd.DataFrame)
-        self._transitions = transitions
+        self._transitions = {
+            subshell: df.convert_dtypes() for subshell, df in transitions.items()
+        }
 
     @classmethod
     def from_ace(cls, ace):